Abstract: Current studies on calcite surface wettability primarily focus on experimental approaches, with limited mechanistic investigations, particularly those neglecting the integrity of crude oil and the initial oil-wet conditions of reservoir surfaces, This research employs molecular dynamics simulations to explore the microscopic mechanisms of wettability alteration induced by water flooding on calcite surfaces coated with single-component and mixed oil molecules. The findings reveal a three-stage process for wettability alteration: Stage 1: Formation of water channels and disruption of the primary oil adsorption layer. Stage 2: Water spreading and displacement along the surface driven by hydrogen bonding interactions (hydrogen bond count increased from 2 to 302). The equilibrium time for mixed oil molecules in this stage is approximately six times longer than that of alkanes. Stage 3: Adsorption equilibrium among oil, water, and the surface. Mixed oil molecules exhibit stronger hydrogen bond energy (H(C₂₇H₂₃O₂N₁)-O(CaCO₃) distance: 1.424Å) compared to water–surface interactions (O(CaCO₃)–H(H₂O): 2.273Å), preventing complete detachment. However, water molecules induce a structural transition in adsorbed oil from lamellar to droplet-like configurations, enhancing water-wetness and reducing oil adhesion probability. These insights provide theoretical guidance for improving water flooding recovery in carbonate reservoirs.